5YCE

Sperm whale myoglobin swMb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.77 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tracing whale myoglobin evolution by resurrecting ancient proteins.

Isogai, Y.Imamura, H.Nakae, S.Sumi, T.Takahashi, K.I.Nakagawa, T.Tsuneshige, A.Shirai, T.

(2018) Sci Rep 8: 16883-16883

  • DOI: 10.1038/s41598-018-34984-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of divin ...

    Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.


    Organizational Affiliation

    Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan. yisogai@pu-toyama.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter macrocephalusMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.77 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.180α = 90.00
b = 30.660β = 105.49
c = 63.570γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP17H01818
Japan Agency for Medical Research and DevelopmentJapan17am0101069j0001

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references